Mariusz Klobukowski

Professor
BSc, PhD, N. Copernicus University, Poland


W3-45 Chemistry Centre
(780) 492-2568
mariusz.klobukowski@ualberta.ca

Group website:
coming soon

 


Our research is focused on the development and applications of methods for accurate computational studies of electronic structure, geometry, vibrational spectra, reaction mechanisms, and one-electron properties of organometallic molecules, molecular ions, and molecular clusters in their ground and excited electronic states. We are interested in both small and lage molecules. For small systems we are using all-electron techniques; for larger molecular systems we use pseudopotential methods. In our work we study systems of very different sizes, from atoms to proteins.

We are specifically interested in:

  • Development, calibration, and applications of pseudopotential methods required to deal with large molecules or molecular systems containing heavy atoms; our model core potentials allow for the description of the scalar relativistic effects.
  • Development and applications of methods to calculate both 1- and 2-electron spin-orbit effects.
  • Development of basis sets for all-electron relativistic calculations on molecules containing very heavy, trans-uranium atoms.
  • Studies of molecular structure and properties of very large molecules and molecular clusters using both non-relativistic and scalar-relativistic model core potential representation of the core electrons and correlated wavefunctions or density functionals for the description of the valence electrons. We are particularly interested in the interactions of such systems with metal ions.
  • Studies of weakly bonded systems containing noble gas atoms in ground end excited electronic states.
  • Studies of novel compounds that contain noble-gas elements. After investigations of molecules with Xe-C bond, we are currently modeling systems that contain xenon and transition metal atoms.
  • Modeling of novel anti-cancer drugs. In this case, in order to be able to represent both the drug molecule as well as the target protein, we use the hybrid QM/MM approach, with the quantum mechanical treatment used for the drug molecule, and molecular mechanics used to model protein.

Figure 1. Contour diagrams of occupied frontier molecular orbitals of Au+Xe, with the maximum contour value 1.0 a.u. and maximum number of contours 100. Red indicates positive sign of the orbitals and blue - negative. [J. Phys. Chem. A, 112 (2008) 5236-5242].

Figure 2. Differences in the binding energies of sixteen derivatives of colchicine (1-16) and ten isoforms of α/β tubulin dimer (I - VIII). Negative values indicate that the derivative binds to tubulin more strongly than colchicine. [J. Chem. Inf. Model. 48 (2008) 1824-1832.]


Selected Publications


Hirotoshi Mori, Tao Zeng, and Mariusz Klobukowski "Assessment of chemical core potentials for the computation on enthalpies of formation of transition-metal complexes" Chem. Phys. Lett., 521 (2012) 150-156.

Tao Zeng, Dmitri G. Fedorov, Michael W. Schmidt, and Mariusz Klobukowski "Effects of spin-orbit coupling on covalent bonding and the Jahn-Teller effect are revealed with the natural language of spinors" J. Chem. Theory Comput., 7 (2011) 2864-2875

Evan Kelly, Jack Tuszynski, and Mariusz Klobukowski "QM and QM/MD Simulations of the Vinca Alkaloids Docked to Tubulin" J. Molec. Graphics Model., 30 (2011) 54-66

Jocelyne Shim, Mariusz Klobukowski, Maria Barysz, and Jerzy Leszczynski "Calibration and applications of †MP2 method for calculating core electron binding energies" Phys. Chem. Chem. Phys., 13 (2011) 5703-5711

Jonathan Y. Mane and Mariusz Klobukowski "New parameterization of PM3 method for monosaccharides" Chem. Phys. Lett., 500 (2010) 1-184

Amelia Fitzsimmons, Hirotoshi Mori, Eisaku Miyoshi, and Mariusz Klobukowski "Model core potential studies of molecules containing rare gas atoms" J. Phys. Chem. A, 114 (2010) 8786-8792

Melissa Gajewski and Mariusz Klobukowski "DFT studies of complexes between ethylenediamine tetraacetate and alkali and alkaline earth cations" Can. J. Chem., 87 (2009) 1492-1498

Tao Zeng, Dmitri Fedorov, and Mariusz Klobukowski "Model core potentials for studies of scalar relativistic effects and spin-orbit coupling at Douglas-Kroll level. I. Theory and applications to Pb and Bi" J. Chem. Phys., 131 (2009) 124109-1 -- 124109-17

Hirotoshi Mori, Kaori Ueno-Noto, You Osanai, Takeshi Noro, Takayuki Fujiwara, Mariusz Klobukowski, and Eisaku Miyoshi "Revised model core potentials for third-row transition-metal atoms from Lu to Hg" Chem. Phys. Lett., 476 (2009) 317-322

J. Y. Mane, M. Klobukowski, J. T. Huzil, and J. Tuszynski "Free energy calculations on the binding of colchicine and its derivatives with the α/β -tubulin isoforms" J. Chem. Inf. Model. 48 (2008) 1824-1832.

T. Zeng and M. Klobukowski, "Relativistic Model Core Potential Study of the Au+Xe System" J. Phys. Chem. A, 112 (2008) 5236-5242.